cluster:73
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cluster:73 [2022/06/28 12:12] hmeij07 [Miniconda3] |
cluster:73 [2022/12/01 13:57] hmeij07 [HPC SDK] |
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| on either cottontail2 or node n33 located at / | on either cottontail2 or node n33 located at / | ||
| Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
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| + | |||
| + | |||
| + | ====== Trimmomatic ====== | ||
| + | |||
| + | * http:// | ||
| + | * binary download and stage | ||
| + | |||
| + | < | ||
| + | |||
| + | / | ||
| + | [root@cottontail Trimmomatic-0.39]# | ||
| + | total 176 | ||
| + | drwxr-xr-x 2 root root 8 Apr 8 2019 adapters | ||
| + | -rw-r--r-- 1 root root 35147 May 16 2018 LICENSE | ||
| + | -rw-r--r-- 1 root root 128502 Apr 8 2019 trimmomatic-0.39.jar | ||
| + | |||
| + | </ | ||
| Line 223: | Line 241: | ||
| Suite of tools for high-accuracy basecaling, assembly, polishing, and alignment. Installed in a specific miniconda3 environment (see below). | Suite of tools for high-accuracy basecaling, assembly, polishing, and alignment. Installed in a specific miniconda3 environment (see below). | ||
| - | * Requires centos7 so queues mwgpu, amber128, exx96 | + | * Requires centos7 so queues mwgpu, |
| * debug server greentail52 | * debug server greentail52 | ||
| * PREFIX=/ | * PREFIX=/ | ||
| Line 233: | Line 251: | ||
| < | < | ||
| - | # environment | + | # environment |
| source / | source / | ||
| export PATH=/ | export PATH=/ | ||
| Line 244: | Line 262: | ||
| which conda python pip mpirun gcc cmake | which conda python pip mpirun gcc cmake | ||
| python --version | python --version | ||
| + | |||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | |||
| </ | </ | ||
| Line 319: | Line 345: | ||
| ** Flye ** | ** Flye ** | ||
| - | Somewhat annoying, no miniconda3 package, so local install, use minconda3 | + | Somewhat annoying, no miniconda3 package, so local install, use minconda3 |
| + | |||
| + | * v2.9.1 (October 2022) | ||
| + | * python bin/flye | ||
| + | * change the PATHs accordingly | ||
| + | |||
| + | < | ||
| + | |||
| + | / | ||
| + | 2.9.1-b1780 | ||
| + | |||
| + | </ | ||
| - | * v2.9 | + | * v2.9 (August 2021) |
| * python bin/flye | * python bin/flye | ||
| Line 669: | Line 706: | ||
| IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020 | IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020 | ||
| + | |||
| + | </ | ||
| + | |||
| + | * https:// | ||
| + | * calterlab, annika (used pip to install) | ||
| + | |||
| + | < | ||
| + | |||
| + | Successfully installed | ||
| + | GridDataFormats-1.0.1 MDAnalysis-2.3.0 | ||
| + | fasteners-0.18 mmtf-python-1.1.3 | ||
| + | mrcfile-1.4.3 msgpack-1.0.4 numpy-1.23.4 | ||
| </ | </ | ||
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| ====== Amber ====== | ====== Amber ====== | ||
| + | |||
| + | ** Amber 22 ** | ||
| + | |||
| + | Details on how to run on CentOS7 can be found at | ||
| + | |||
| + | * https:// | ||
| ** Amber 20 ** | ** Amber 20 ** | ||
cluster/73.txt · Last modified: 2024/02/16 11:17 by hmeij07
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